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Fix documentation
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trex.org
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trex.org
@ -46,17 +46,21 @@ I/O as for ~sparse~ data but without the need to write indices of the sparse val
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For determinant lists (integer bit fields), the ~special~ attribute is present in the type.
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This means that the source code is not produced by the generator, but hand-written.
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Some data may be complex. In that case, the real part should be stored
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in the variable, and the imaginary part will be stored in the variable
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with the same name suffixed by ~_im~.
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#+begin_src python :tangle trex.json :exports none
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{
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#+end_src
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* Metadata (metadata group)
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As we expect our files to be archived in open-data repositories, we
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need to give the possibility to the users to store some metadata
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inside the files. We propose to store the list of names of the codes
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which have participated to the creation of the file, a list of
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authors of the file, and a textual description.
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As we expect TREXIO files to be archived in open-data repositories,
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we give the possibility to the users to store some metadata inside
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the files. We propose to store the list of names of the codes which
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have participated to the creation of the file, a list of authors of
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the file, and a textual description.
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#+NAME: metadata
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| Variable | Type | Dimensions (for arrays) | Description |
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@ -69,7 +73,7 @@ This means that the source code is not produced by the generator, but hand-writt
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| ~description~ | ~str~ | | Text describing the content of file |
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| ~unsafe~ | ~int~ | | ~1~: true, ~0~: false |
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**Note:** ~unsafe~ attribute of the ~metadata~ group indicates
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**Note:** The ~unsafe~ attribute of the ~metadata~ group indicates
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whether the file has been previously opened with ~'u'~ mode. It is
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automatically written in the file upon the first unsafe opening. If
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the user has checked that the TREXIO file is valid (e.g. using
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@ -181,7 +185,7 @@ This means that the source code is not produced by the generator, but hand-writt
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The structure of this group is adapted for the [[https://github.com/dftlibs/numgrid][numgrid]] library.
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Feel free to submit a PR if you find missing options/functionalities.
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#+name: grid
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#+NAME: grid
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| Variable | Type | Dimensions | Description |
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|-----------------+---------+------------------+-------------------------------------------------------------------------|
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| ~description~ | ~str~ | | Details about the used quadratures can go here |
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@ -485,23 +489,25 @@ prim_factor =
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| ~power~ | ~int~ | ~(ecp.num)~ | $n_{A q \ell}$ all ECP powers |
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There might be some confusion in the meaning of the $\ell_{\max}$.
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It can be attributed to the maximum angular momentum occupied
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in the core orbitals, which are removed by the ECP.
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On the other hand, it can be attributed to the maximum angular momentum of the
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ECP that replaces the core electrons.
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*Note*, that the latter $\ell_{\max}$ is always higher by 1 than the former.
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*Note for developers*: avoid having variables with similar prefix in their name.
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HDF5 back end might cause issues due to the way ~find_dataset~ function works.
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For example, in the ECP group we use ~max_ang_mom~ and not ~ang_mom_max~.
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The latter causes issues when written before the ~ang_mom~ array in the TREXIO file.
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*Update*: in fact, the aforementioned issue has only been observed when using HDF5 version 1.10.4
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installed via ~apt-get~. Installing the same version from the ~conda-forge~ channel and running it in
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an isolated ~conda~ environment works just fine. Thus, it seems to be a bug in the ~apt~-provided package.
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If you encounter the aforementioned issue, please report it to our [[https://github.com/TREX-CoE/trexio/issues][issue tracker on GitHub]].
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There might be some confusion in the meaning of the $\ell_{\max}$.
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It can be attributed to the maximum angular momentum occupied in
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the core orbitals, which are removed by the ECP. On the other
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hand, it can be attributed to the maximum angular momentum of the
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ECP that replaces the core electrons.
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*Note*, that the latter $\ell_{\max}$ is always higher by 1 than the former.
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*Note for developers*: avoid having variables with similar prefix
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in their name. The HDF5 back end might cause issues due to the way
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~find_dataset~ function works. For example, in the ECP group we
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use ~max_ang_mom~ and not ~ang_mom_max~. The latter causes issues
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when written before the ~ang_mom~ array in the TREXIO file.
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*Update*: in fact, the aforementioned issue has only been observed
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when using HDF5 version 1.10.4 installed via ~apt-get~. Installing
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the same version from the ~conda-forge~ channel and running it in
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an isolated ~conda~ environment works just fine. Thus, it seems to
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be a bug in the ~apt~-provided package.
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If you encounter the aforementioned issue, please report it to our
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[[https://github.com/TREX-CoE/trexio/issues][issue tracker on GitHub]].
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#+CALL: json(data=ecp, title="ecp")
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@ -663,18 +669,18 @@ power = [
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over atomic orbitals.
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#+NAME: ao_1e_int
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| Variable | Type | Dimensions | Description |
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|-----------------------+---------+--------------------+-----------------------------------------------------------------------------------|
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| ~overlap~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert q \rangle$ (real part, general case) |
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| ~kinetic~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{T}_e \vert q \rangle$ (real part, general case) |
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| ~potential_n_e~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ne}} \vert q \rangle$ (real part, general case) |
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| ~ecp~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ecp}} \vert q \rangle$ (real part, general case) |
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| ~core_hamiltonian~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{h} \vert q \rangle$ (real part, general case) |
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| ~overlap_im~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert q \rangle$ (imaginary part) (imaginary part) |
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| ~kinetic_im~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{T}_e \vert q \rangle$ (imaginary part) |
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| ~potential_n_e_im~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ne}} \vert q \rangle$ (imaginary part) |
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| ~ecp_im~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ECP}} \vert q \rangle$ (imaginary part) |
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| ~core_hamiltonian_im~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{h} \vert q \rangle$ (imaginary part) |
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| Variable | Type | Dimensions | Description |
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|-----------------------+---------+--------------------+--------------------------------------------------------------------------|
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| ~overlap~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert q \rangle$ |
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| ~kinetic~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{T}_e \vert q \rangle$ |
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| ~potential_n_e~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ne}} \vert q \rangle$ |
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| ~ecp~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ecp}} \vert q \rangle$ |
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| ~core_hamiltonian~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{h} \vert q \rangle$ |
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| ~overlap_im~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert q \rangle$ (imaginary part) |
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| ~kinetic_im~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{T}_e \vert q \rangle$ (imaginary part) |
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| ~potential_n_e_im~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ne}} \vert q \rangle$ (imaginary part) |
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| ~ecp_im~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{V}_{\text{ECP}} \vert q \rangle$ (imaginary part) |
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| ~core_hamiltonian_im~ | ~float~ | ~(ao.num, ao.num)~ | $\langle p \vert \hat{h} \vert q \rangle$ (imaginary part) |
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#+CALL: json(data=ao_1e_int, title="ao_1e_int")
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@ -716,11 +722,21 @@ power = [
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\sum_{j=1}^{i-1} \frac{\text{erf}(\vert \mathbf{r}_i -
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\mathbf{r}_j \vert)}{\vert \mathbf{r}_i - \mathbf{r}_j \vert} \] : electron-electron long range potential
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The Cholesky decomposition of the integrals can also be stored:
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\[
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A_{ijkl} = \sum_{\alpha} G_{il\alpha} G_{jl\alpha}
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\]
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#+NAME: ao_2e_int
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| Variable | Type | Dimensions | Description |
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|----------+----------------+------------------------------------+-----------------------------------------|
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| ~eri~ | ~float sparse~ | ~(ao.num, ao.num, ao.num, ao.num)~ | Electron repulsion integrals |
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| ~eri_lr~ | ~float sparse~ | ~(ao.num, ao.num, ao.num, ao.num)~ | Long-range Electron repulsion integrals |
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| Variable | Type | Dimensions | Description |
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|-----------------------+----------------+---------------------------------------------------+-----------------------------------------------|
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| ~eri~ | ~float sparse~ | ~(ao.num, ao.num, ao.num, ao.num)~ | Electron repulsion integrals |
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| ~eri_lr~ | ~float sparse~ | ~(ao.num, ao.num, ao.num, ao.num)~ | Long-range Electron repulsion integrals |
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| ~eri_cholesky_num~ | ~dim~ | | Number of Cholesky vectors for ERI |
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| ~eri_cholesky~ | ~float sparse~ | ~(ao.num, ao.num, ao_2e_int.eri_cholesky_num)~ | Cholesky decomposition of the ERI |
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| ~eri_lr_cholesky_num~ | ~dim~ | | Number of Cholesky vectors for long range ERI |
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| ~eri_lr_cholesky~ | ~float sparse~ | ~(ao.num, ao.num, ao_2e_int.eri_lr_cholesky_num)~ | Cholesky decomposition of the long range ERI |
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#+CALL: json(data=ao_2e_int, title="ao_2e_int")
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@ -728,8 +744,12 @@ power = [
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:results:
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#+begin_src python :tangle trex.json
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"ao_2e_int": {
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"eri" : [ "float sparse", [ "ao.num", "ao.num", "ao.num", "ao.num" ] ]
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, "eri_lr" : [ "float sparse", [ "ao.num", "ao.num", "ao.num", "ao.num" ] ]
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"eri" : [ "float sparse", [ "ao.num", "ao.num", "ao.num", "ao.num" ] ]
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, "eri_lr" : [ "float sparse", [ "ao.num", "ao.num", "ao.num", "ao.num" ] ]
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, "eri_cholesky_num" : [ "dim" , [] ]
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, "eri_cholesky" : [ "float sparse", [ "ao_2e_int.eri_cholesky_num", "ao.num", "ao.num" ] ]
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, "eri_lr_cholesky_num" : [ "dim" , [] ]
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, "eri_lr_cholesky" : [ "float sparse", [ "ao_2e_int.eri_lr_cholesky_num", "ao.num", "ao.num" ] ]
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} ,
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#+end_src
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:end:
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@ -741,8 +761,8 @@ power = [
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|------------------+---------+--------------------+--------------------------------------------------------------------------|
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| ~type~ | ~str~ | | Free text to identify the set of MOs (HF, Natural, Local, CASSCF, /etc/) |
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| ~num~ | ~dim~ | | Number of MOs |
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| ~coefficient~ | ~float~ | ~(ao.num, mo.num)~ | MO coefficients (real part, general case) |
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| ~coefficient_im~ | ~float~ | ~(ao.num, mo.num)~ | MO coefficients (imaginary part, for periodic calculations) |
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| ~coefficient~ | ~float~ | ~(ao.num, mo.num)~ | MO coefficients |
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| ~coefficient_im~ | ~float~ | ~(ao.num, mo.num)~ | MO coefficients (imaginary part) |
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| ~class~ | ~str~ | ~(mo.num)~ | Choose among: Core, Inactive, Active, Virtual, Deleted |
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| ~symmetry~ | ~str~ | ~(mo.num)~ | Symmetry in the point group |
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| ~occupation~ | ~float~ | ~(mo.num)~ | Occupation number |
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@ -775,18 +795,18 @@ power = [
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the basis of molecular orbitals.
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#+NAME: mo_1e_int
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| Variable | Type | Dimensions | Description |
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|-----------------------+---------+--------------------+-----------------------------------------------------------------------------------|
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| ~overlap~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert j \rangle$ (real part, general case) |
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| ~kinetic~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{T}_e \vert j \rangle$ (real part, general case) |
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| ~potential_n_e~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{V}_{\text{ne}} \vert j \rangle$ (real part, general case) |
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| ~ecp~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{V}_{\text{ECP}} \vert j \rangle$ (real part, general case) |
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| ~core_hamiltonian~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{h} \vert j \rangle$ (real part, general case) |
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| ~overlap_im~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert j \rangle$ (imaginary part) (imaginary part) |
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| ~kinetic_im~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{T}_e \vert j \rangle$ (imaginary part) |
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| ~potential_n_e_im~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{V}_{\text{ne}} \vert j \rangle$ (imaginary part) |
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| ~ecp_im~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{V}_{\text{ECP}} \vert j \rangle$ (imaginary part) |
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| ~core_hamiltonian_im~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{h} \vert j \rangle$ (imaginary part) |
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| Variable | Type | Dimensions | Description |
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|-----------------------+---------+--------------------+--------------------------------------------------------------------------|
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| ~overlap~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert j \rangle$ |
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| ~kinetic~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{T}_e \vert j \rangle$ |
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| ~potential_n_e~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{V}_{\text{ne}} \vert j \rangle$ |
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| ~ecp~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{V}_{\text{ECP}} \vert j \rangle$ |
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| ~core_hamiltonian~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{h} \vert j \rangle$ |
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| ~overlap_im~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert j \rangle$ (imaginary part) |
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| ~kinetic_im~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{T}_e \vert j \rangle$ (imaginary part) |
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| ~potential_n_e_im~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{V}_{\text{ne}} \vert j \rangle$ (imaginary part) |
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| ~ecp_im~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{V}_{\text{ECP}} \vert j \rangle$ (imaginary part) |
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| ~core_hamiltonian_im~ | ~float~ | ~(mo.num, mo.num)~ | $\langle i \vert \hat{h} \vert j \rangle$ (imaginary part) |
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#+CALL: json(data=mo_1e_int, title="mo_1e_int")
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@ -814,12 +834,6 @@ power = [
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[[#ao_two_e][AO two-electron integrals section]]. Here, the integrals are given in
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the basis of molecular orbitals.
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The Cholesky decomposition of the integrals can also be stored:
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\[
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A_{ijkl} = \sum_{\alpha} G_{il\alpha} G_{jl\alpha}
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\]
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#+NAME: mo_2e_int
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| Variable | Type | Dimensions | Description |
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|-----------------------+----------------+---------------------------------------------------+-----------------------------------------------|
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@ -845,18 +859,6 @@ power = [
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} ,
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#+end_src
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:end:
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:results:
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#+begin_src python :tangle trex.json
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"mo_2e_int": {
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"eri" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ]
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, "eri_lr" : [ "float sparse", [ "mo.num", "mo.num", "mo.num", "mo.num" ] ]
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, "eri_cholesky_num" : [ "dim" , [] ]
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, "eri_cholesky" : [ "float sparse", [ "mo_2e_int.eri_cholesky_num", "mo.num", "mo.num" ] ]
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, "eri_lr_cholesky_num" : [ "dim" , [] ]
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, "eri_lr_cholesky" : [ "float sparse", [ "mo_2e_int.eri_lr_cholesky_num", "mo.num", "mo.num" ] ]
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} ,
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#+end_src
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:
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* N-electron basis
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** Slater determinants (determinant group)
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@ -1228,7 +1230,7 @@ power = [
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| ~en_nucleus~ | ~index~ | ~(jastrow.en_num)~ | Nucleus relative to the eN parameter |
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| ~een_nucleus~ | ~index~ | ~(jastrow.een_num)~ | Nucleus relative to the eeN parameter |
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| ~ee_scaling~ | ~float~ | | $\kappa$ value in CHAMP Jastrow for electron-electron distances |
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| ~eN_scaling~ | ~float~ | ~(nucleus.num)~ | $\kappa$ value in CHAMP Jastrow for electron-nucleus distances |
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| ~en_scaling~ | ~float~ | ~(nucleus.num)~ | $\kappa$ value in CHAMP Jastrow for electron-nucleus distances |
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* Quantum Monte Carlo data (qmc group)
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